lindenb / jvarkitLinks
Java utilities for Bioinformatics
☆504Updated 3 weeks ago
Alternatives and similar repositories for jvarkit
Users that are interested in jvarkit are comparing it to the libraries listed below
Sorting:
- Plot structural variant signals from many BAMs and CRAMs☆544Updated last year
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆425Updated 2 months ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆475Updated 2 weeks ago
- Transcript assembly and quantification for RNA-Seq☆449Updated 3 weeks ago
- Count bases in BAM/CRAM files☆319Updated 3 years ago
- Graph-based alignment (Hierarchical Graph FM index)☆503Updated 8 months ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆444Updated last year
- This Snakemake pipeline implements the GATK best-practices workflow☆254Updated 2 years ago
- Tools to process and analyze deep sequencing data.☆723Updated last week
- ☆279Updated 5 months ago
- Tools for working with genomic and high throughput sequencing data.☆334Updated this week
- BEDOPS: high-performance genomic feature operations☆343Updated 2 months ago
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆513Updated 4 months ago
- C++ API & command-line toolkit for working with BAM data☆425Updated last month
- Customizable workflows based on snakemake and python for the analysis of NGS data☆399Updated 3 weeks ago
- This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.☆242Updated 2 years ago
- RNA-seq workflow using STAR and DESeq2☆342Updated 11 months ago
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆271Updated last year
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆422Updated 6 months ago
- Structural variation caller using third generation sequencing☆603Updated last week
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆389Updated 7 months ago
- TransDecoder source☆292Updated 9 months ago
- Tools for handling Unique Molecular Identifiers in NGS data sets☆515Updated this week
- annotate a VCF with other VCFs/BEDs/tabixed files☆379Updated 2 weeks ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆320Updated last month
- Documentation for the ANNOVAR software☆242Updated last week
- Differential analysis of RNA-Seq☆305Updated last month
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆495Updated this week
- Haplotype VCF comparison tools☆437Updated last year
- lumpy: a general probabilistic framework for structural variant discovery☆331Updated 3 years ago